Similar studies for GEO DataSets (Select 200077565) - GEO DataSets

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Items: 20

Select item 2000775651.

Genome-wide chromosomal conformation elucidates regulatory relationships in human brain development and disease

(Submitter supplied) The demonstration that chromatin exhibits a complex 3 dimensional organization, whereby short and long distance physical interactions correspond to complex gene regulatory processes has opened a new window on understanding the functional organization of the human genome. Recently, chromatin remodeling has also been causally implicated in several neurodevelopmental disorders, including autism and schizophrenia. more...

Organism:: Homo sapiens

Type:: Other

Platform:: GPL11154
6 Samples

Download data: BED, HDF5

Series

Accession:: GSE77565

ID:: 200077565

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000395102.

Chromatin Interactions by 5C from ENCODE/Dekker Univ. Mass.

(Submitter supplied) Amartya Sanyal mailto:[email protected] (Wet Lab), Bryan R. Lajoie mailto:[email protected], Gaurav Jain mailto:[email protected] (Dry Lab), Job Dekker mailto:[email protected] (Principal Investigator) This track contains chromatin interaction data generated using the 5C (Chromatin Conformation Capture Carbon Copy) method by the ENCODE group (Dekker Lab) located at the University of Massachusetts, Worcester, MA. more...

Organism:: Homo sapiens

Type:: Other

Platform:: GPL9052
4 Samples

Download data: BED, MATRIX, TXT

Series

Accession:: GSE39510

ID:: 200039510

PubMed Full text in PMC Similar studies ENCODE SRA Run Selector

Select item 2000894413.

Systematic analysis of chromatin interactions at disease associated loci links novel candidate genes to inflammatory bowel disease

(Submitter supplied) Background: Genome wide association studies (GWASs) have revealed many susceptibility loci for complex genetic diseases. For most loci the causal genes have not been identified. The identification of candidate genes is currently mainly based genes that localize close to or within the identified loci. We have recently shown that 92 of the 163 Inflammatory Bowel Disease (IBD)-loci co-localize with noncoding DNA regulatory elements (DRE). more...

Organism:: Homo sapiens

Type:: Other

Platform:: GPL16791
372 Samples

Download data: WIG

Series

Accession:: GSE89441

ID:: 200089441

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000833454.

Open chromatin profiling of human postmortem brain infers functional roles for non-coding schizophrenia loci

(Submitter supplied) Open chromatin provides access to DNA binding proteins for the correct spatiotemporal regulation of gene expression. Mapping chromatin accessibility has been widely used to identify the location of cis regulatory elements (CREs) including promoters and enhancers. CREs show tissue- and cell-type specificity and disease-associated variants are often enriched for CREs in the tissues and cells that pertain to a given disease. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL16791
16 Samples

Download data: BW

Series

Accession:: GSE83345

ID:: 200083345

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001168255.

Robust Hi-C maps of enhancer-promoter interactions reveal the function of non-coding genome in neural development and diseases

(Submitter supplied) Genome-wide mapping of chromatin interactions at high resolution remains experimentally and computationally challenging. Here we used a low-input “easy Hi-C” protocol to map the 3D genome architecture in human neurogenesis and brain tissues and also demonstrated that a rigorous Hi-C bias-correction pipeline (HiCorr) can significantly improve the sensitivity and robustness of Hi-C loop identification at sub-TAD level, especially the enhancer-promoter (E-P) interactions. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:: GPL16791
24 Samples

Download data: BED, TXT

Series

Accession:: GSE116825

ID:: 200116825

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001154076.

Robust Hi-C maps of enhancer-promoter interactions reveal the function of non-coding genome in neural development and diseases

(Submitter supplied) Despite recent progress in mammalian 3D genome studies, it remains experimentally and computationally challenging to identify chromatin interactions genome-wide. Here we developed a highly efficient “easy Hi-C” (eHi-C) protocol that generates high-yield libraries with 0.1 million cells. After rigorous bias-correction with a significantly improved Hi-C analysis pipeline, we can directly recognize the dynamic long- and short-range chromatin loops from contact heatmaps. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing; Other; Third-party reanalysis; Expression profiling by high throughput sequencing

Platforms:: GPL20301 GPL20795 GPL16791
40 Samples

Download data: BED, TXT, XLSX

Series

Accession:: GSE115407

ID:: 200115407

PubMed Full text in PMC Similar studies Analyze with GEO2R SRA Run Selector

Select item 2000893247.

Easy Hi-C: A simple efficient protocol for 3D genome mapping in small cell populations

(Submitter supplied) Despite the growing interest in studying the mammalian genome organization, it is still challenging to map the DNA contacts genome-wide. Here we present easy Hi-C (eHi-C), a highly efficient method for unbiased mapping of 3D genome architecture. The eHi-C protocol only involves a series of enzymatic reactions and maximizes the recovery of DNA products from proximity ligation. We show that eHi-C can be performed with 0.1 million cells and yields high quality libraries comparable to Hi-C.

Organism:: Homo sapiens

Type:: Other

Platforms:: GPL15520 GPL11154
10 Samples

Download data: TXT

Series

Accession:: GSE89324

ID:: 200089324

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001573068.

Integrative analysis of liver-specific noncoding regulatory variants associated with the risk of coronary artery disease

(Submitter supplied) We performed promoter Capture Hi-C in HepG2 to investigate interactions between gene promoters and distal elements as a transcription-regulating mechanism contributing to these phenotypes. We also performed ChIP-Seq at 2h, 8h and 23h timepoints in HepG2 for Il1B treatment.

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL20301 GPL11154
10 Samples

Download data: BIGWIG, TXT

Series

Accession:: GSE157306

ID:: 200157306

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000712789.

Parkinson-associated risk variant in distal enhancer of α-synuclein modulates target gene expression

(Submitter supplied) Genome-wide association studies (GWAS) have identified genomic loci associated with complex diseases but mechanistic insights are impeded by the lack of understanding of how specific risk variants functionally contribute to diseases. Here we describe an experimental strategy to robustly identify cis-acting effects of genetic variants in regulatory elements on gene expression by combining genome-wide epigenetic information with CRISPR/Cas genome editing in human pluripotent cells. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL11154
11 Samples

Download data: WIG

Series

Accession:: GSE71278

ID:: 200071278

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20013275710.

CRISPR-Mediated Multiplexed Epigenomic Perturbation of Putatively Functional ASoC Sites in Human Neural Progenitor Cell Model at Single-cell Resolution

(Submitter supplied) Functional interpretation of noncoding disease variants, which likely regulate gene expression, has been challenging. Chromatin accessibility (openness) strongly influences gene expression in neurodevelopment; however, to what extent genetic variants can alter chromatin openness in the context of brain disorders/traits is largely unknown. Using human induced pluripotent stem cell (iPSC)-derived neurons as a neurodevelopmental model, we identified abundant open-chromatin regions absent in brains and thousands of genetic variants exhibiting allele-specific open-chromatin (ASoC). more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
2 Samples

Download data: H5

Series

Accession:: GSE132757

ID:: 200132757

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20012901711.

Allele-specific open chromatin in human neurons elucidates functional noncoding disease variants

(Submitter supplied) ASoC variants are prevalent and cell type-specific ASoC variants were over-represented in intergenic regions and active enhancers. The collection includes ATAC-Seq and RNA-Seq data that were taken from human iPS cells and their derived neuronal cells (neural progenitor cells, cortical glutamatergic neurons, GABAergic neurons, and dopaminergic neurons).

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL24676 GPL11154
118 Samples

Download data: BED, TXT

Series

Accession:: GSE129017

ID:: 200129017

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20006239112.

A role for non-coding variation in schizophrenia

(Submitter supplied) A large portion of common variant loci associated with genetic risk for schizophrenia reside within non-coding sequence of unknown function. Here, we demonstrate promoter and enhancer enrichment in schizophrenia variants associated with expression quantitative trait loci (eQTL). The enrichment is greater when functional annotations derived from human brain are used relative to peripheral tissues. Regulatory trait concordance analysis ranked genes within schizophrenia genome-wide significant loci, based on co-localization of a risk SNP, eQTL and regulatory element sequence. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL9115
3 Samples

Download data: TXT

Series

Accession:: GSE62391

ID:: 200062391

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20026684413.

pooled clone sequencing from DNA cloning sample (ENCSR992PQH)

(Submitter supplied) For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf